Table 3 Quantitative trait loci (QTL) surpassing the significance threshold (P < 5 × 10−7) for evidence of an association with the diffuse lesions.

From: Identification of loci associated with pathological outcomes in Holstein cattle infected with Mycobacterium avium subsp. paratuberculosis using whole-genome sequence data

BTA1

QTL start (bp)

QTL end (bp)

P value most significant SNP

SNP position2

Annotation

Genes in QTL3

No of significant SNPs in QTL

1

97006475

98111140

2.78E−07

97523460

Intergenic

SLC7A14, CLDN11, SKIL, PRKCI, U2, PHC3, U6, GPR160, SEC62, SAMD7, LRRIQ4, LRRC34, MYNN, ACTRT3, Telomerase-vert, ENSBTAG00000049676, ENSBTAG00000042535, ENSBTAG00000045991, ENSBTAG00000053891, ENSBTAG00000047144

35

1

93955885

94925704

4.30E−07

94425704

Intron

SPATA16, ECT2, NCEH1

8

3

63439078

64439078

3.16E−07

63939078

Upstream

U6, ENSBTAG00000052602

1

7

15613384

17275615

2.91E−09

16113384

Intron

PDE4A, KEAP1, s1PR5, ATG4D, KRI1, CDKN2D, AP1M2, SLC44A2, ILF3, QTRT1, DNM2, TMED1, C7H19orf38, CARM1, bta-mir3604-1, YIPF2, SMARCA4, TIMM29, TMED1, SPC24, KANK2,5S_rRNA, U6, LDLR, RAB3D, TMEM205, CCDC159, DOCK6, ANGPTL8, ELAVL3, ELOF1, PLPPR2, ACP5, EPOR, RGL3, ODAD3, PRKCSH, ZNF653, ECSIT, U4, INSR, ZNF557, ARHGEF18, CAMSAP3, PEX11G, RETN, XAB2, TEX45, MCEMP1, PET100, ZNF358, MCOLN1, PNPLA6, PCP2, STXBP2, TRAPPC5, FCER2, LRRC8B, CD209, MAP2K7, CLEC4G, EVI5L, CCL25, SNAPC2, TIMM44, bta-mir-2455, ELAVL1, FBN3, MARCHF2, CERS4, HNRNPM, ADAMTS10, bta-mir-339b, ANGPTL4, ACTL9, CD320, PRAM1, NDUFA7, ZNF414, RAB11B, OR2Z1, RPS28, MYO1F, SNORA70, ENSBTAG00000051140, ENSBTAG00000051490, ENSBTAG00000054591, ENSBTAG00000046336, ENSBTAG00000038680, ENSBTAG00000047612, ENSBTAG00000044018, ENSBTAG00000052882, ENSBTAG00000049668, ENSBTAG00000054873

21

7

26041927

27059884

1.12E−07

26547965

Intergenic

CCDC192, 5S_rRNA, bta-mir-12007, CTXN3, PRRC1, MEGF10, U6, C7H5orf63, MARCHF3, ENSBTAG00000051246

12

7

23796173

25086968

1.73E−07

24296173

Intergenic

CHSY3, MINAR2, ADAMTS19, ISOC1, SLC27A6, ENSBTAG00000051108, ENSBTAG00000051190

4

8

77894983

78394983

9.77E−09

78394983

Intergenic

NTRK2

2

13

66829928

68799183

4.70E−10

67404014

Intron

VSTM2L, TTI1, RPRD1B, TGM2, U6, LIAA1755, BPI, LBP, SNORA71, RALGAPB, ADIG, SLC32A1, ACTR5, PPP1R16B, FAM83D, DHX35, ENSBTAG00000051355, ENSBTAG00000047302, ENSBTAG00000050770, ENSBTAG00000052551, ENSBTAG00000044690

6

23

13569222

14569289

3.91091E−07

14069222

Intergenic

KIF6, DAAM2, MOCS1, U6, LRFN2, ENSBTAG00000048842

3

  1. 1QTL location, 2SNP location in the genome assembly, 3Positional candidate genes are defined as genes that are located within 50 kb on either side of the identified QTL.
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